Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

CA2466438179

Gene: SLC6A8

Condition: creatine transporter deficiency

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 68826926-8ae8-425c-b249-3a1763e03ab7

HGVS expressions

NM_001142805.2:c.1225-35G>A

NC_000023.11:g.153694095G>A

CM000685.2:g.153694095G>A

NC_000023.10:g.152959550G>A

CM000685.1:g.152959550G>A

NC_000023.9:g.152612744G>A

NG_012016.1:g.10799G>A

NG_012016.2:g.10799G>A

ENST00000253122.10:c.1255-35G>A

ENST00000253122.9:c.1255-35G>A

ENST00000413787.1:c.258-109G>A

ENST00000430077.6:c.910-35G>A

ENST00000442457.1:c.309-35G>A

ENST00000457723.1:c.239-42G>A

ENST00000485324.1:n.1365G>A

NM_001142805.1:c.1225-35G>A

NM_001142806.1:c.910-35G>A

NM_005629.3:c.1255-35G>A

NM_005629.4:c.1255-35G>A

Uncertain Significance

BP4 PM2_Supporting

Evidence Links 0

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1.1.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Cerebral Creatine Deficiency Syndromes VCEP

The NM_005629.4:c.1255-35G>A variant in SLC6A8 is an intronic variant affecting a nucleotide within the consensus splice site of intron 8. This variant has been reported as a novel variant in one individual undergoing genetic testing for suspected X-linked intellectual disability (PMID: 15154114), without further specification; thus PP4 does not apply. The variant is absent in gnomAD v2.1.1. (PM2_Supporting). The computational predictors SpliceAI and varSEAK predict that this variant does not impact splicing (BP4). In summary, this variant meets criteria to be classified as a variant of uncertain significance for creatine transporter deficiency. SLC6A8-specific criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): PM2_Supporting, BP4. Curation Expert Panel on March 28, 2024)

BP4

The computational predictors SpliceAI and varSEAK predict that this variant does not impact splicing (BP4)

PM2_Supporting

The variant is absent in gnomAD v2.1.1. (PM2_Supporting).

Approved on: 2024-03-28

Published on: 2024-03-28

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